Something did not work as expected. Please file an issue at https://github.com/easystats/easystats/issues/ and post
the following output:
``check_model()` returned following error: replacement has 1 row, data has 0
If the error message does not help
identifying your problem, another reason why `check_model()` failed might be that
models of class `lm` are not yet
supported.`
| Metric | Value |
|---|---|
| AIC | -Inf |
| AICc | -Inf |
| BIC | -Inf |
| R2 | 1.00 |
| RMSE | 0.00 |
For interpretation of performance metrics, please refer to this documentation.
| Parameter | Coefficient | 95% CI | df |
|---|---|---|---|
| (Intercept) | -10.93 | 0 | |
| b n genera metabarcoding | 0.20 | 0 | |
| c n genera flower count | -8.02e-03 | 0 | |
| period (2) | 1.37 | 0 | |
| period (3) | -3.80 | 0 | |
| period (4) | 5.05 | 0 |
To find out more about table summary options, please refer to this documentation.
| b_n_genera_metabarcoding | Predicted | SE | 95% CI |
|---|---|---|---|
| 1.07 | -11.18 | 0.00 | |
| 22.84 | -6.91 | 0.00 | |
| 44.62 | -2.64 | 0.00 | |
| 66.39 | 1.63 | 0.00 | |
| 88.17 | 5.90 | 0.00 | |
| 109.94 | 10.17 | 0.00 | |
| 131.72 | 14.44 | 0.00 | |
| 153.49 | 18.71 | 0.00 | |
| 175.27 | 22.98 | 0.00 | |
| 197.04 | 27.25 | 0.00 |
Variable predicted: a_n_genera_interactions
Predictors modulated: b_n_genera_metabarcoding
Predictors controlled: c_n_genera_flower_count (58), period (1)
| c_n_genera_flower_count | Predicted | SE | 95% CI |
|---|---|---|---|
| -24.15 | 6.55 | 0.00 | |
| -3.74 | 6.39 | 0.00 | |
| 16.67 | 6.23 | 0.00 | |
| 37.09 | 6.06 | 0.00 | |
| 57.50 | 5.90 | 0.00 | |
| 77.91 | 5.73 | 0.00 | |
| 98.33 | 5.57 | 0.00 | |
| 118.74 | 5.41 | 0.00 | |
| 139.15 | 5.24 | 0.00 | |
| 159.57 | 5.08 | 0.00 |
Variable predicted: a_n_genera_interactions
Predictors modulated: c_n_genera_flower_count
Predictors controlled: b_n_genera_metabarcoding (88), period (1)
| period | Predicted | SE | 95% CI |
|---|---|---|---|
| 1.00 | 5.90 | 0.00 | |
| 2.00 | 7.27 | 0.00 | |
| 3.00 | 2.09 | 0.00 | |
| 4.00 | 10.95 | 0.00 | |
| 5.00 | 5.90 | 0.00 | |
| 6.00 | 5.90 | 0.00 |
Variable predicted: a_n_genera_interactions
Predictors modulated: period
Predictors controlled: b_n_genera_metabarcoding (88), c_n_genera_flower_count (58)
We fitted a linear model (estimated using OLS) to predict a_n_genera_interactions with b_n_genera_metabarcoding, c_n_genera_flower_count and period (formula: a_n_genera_interactions ~ b_n_genera_metabarcoding + c_n_genera_flower_count + factor(period)). The model explains a statistically NA and substantial proportion of variance (R2 = 1.00, F(5, 0) = , ). The model’s intercept, corresponding to b_n_genera_metabarcoding = 0, c_n_genera_flower_count = 0 and period = 0, is at -10.93 (t(0) = ). Within this model:
Standardized parameters were obtained by fitting the model on a standardized version of the dataset. 95% Confidence Intervals (CIs) and p-values were computed using a Wald t-distribution approximation. The model explains a statistically NA and substantial proportion of variance (R2 = 1.00, F(5, 0) = , )
---
title: "Regression model summary from `{easystats}`"
output:
flexdashboard::flex_dashboard:
theme:
version: 4
# bg: "#101010"
# fg: "#FDF7F7"
primary: "#0054AD"
base_font:
google: Prompt
code_font:
google: JetBrains Mono
params:
model: model
check_model_args: check_model_args
parameters_args: parameters_args
performance_args: performance_args
---
```{r setup, include=FALSE}
library(flexdashboard)
library(easystats)
# Since not all regression model are supported across all packages, make the
# dashboard chunks more fault-tolerant. E.g. a model might be supported in
# `{parameters}`, but not in `{report}`.
#
# For this reason, `error = TRUE`
knitr::opts_chunk$set(
error = TRUE,
out.width = "100%"
)
# helper function for printing `{report}` outputs
bracket_to_parantheses <- function(text) {
gsub("]", ")", gsub("[", "(", text, fixed = TRUE), fixed = TRUE)
}
```
```{r easydashboard-1}
# Get user-specified model data
model <- params$model
# Is it supported by `{easystats}`? Skip evaluation of the following chunks if not.
is_supported <- insight::is_model_supported(model)
if (!is_supported) {
unsupported_message <- sprintf(
"Unfortunately, objects of class `%s` are not yet supported in {easystats}.\n
For a list of supported models, see `insight::supported_models()`.",
class(model)[1]
)
}
```
Model fit
=====================================
Column {data-width=700}
-----------------------------------------------------------------------
### Assumption checks
```{r check-model, eval=is_supported, fig.height=10, fig.width=10}
check_model_args <- c(list(model), params$check_model_args)
# add verbose, if not done yet
if (is.null(check_model_args$verbose)) check_model_args$verbose <- FALSE
tryCatch(
{
do.call(performance::check_model, check_model_args)
},
error = function(e) {
cat(insight::format_message(
"\nSomething did not work as expected. Please file an issue at {.url https://github.com/easystats/easystats/issues/} and post the following output:",
paste0("\n`", e$message, "`")
))
}
)
```
```{r easydashboard-2, eval=!is_supported}
cat(unsupported_message)
```
Column {data-width=300}
-----------------------------------------------------------------------
### Indices of model fit
```{r easydashboard-3, eval=is_supported}
# {performance}
performance_args <- c(list(model), params$performance_args)
# add verbose, if not done yet
if (is.null(performance_args$verbose)) performance_args$verbose <- FALSE
table_performance <- do.call(performance::performance, performance_args)
print_md(table_performance, layout = "vertical", caption = NULL)
```
```{r easydashboard-4, eval=!is_supported}
cat(unsupported_message)
```
For interpretation of performance metrics, please refer to <a href="https://easystats.github.io/performance/reference/model_performance.html" target="_blank">this documentation</a>.
Parameter estimates
=====================================
Column {data-width=550}
-----------------------------------------------------------------------
### Plot
```{r dot-whisker, eval=is_supported}
# `{parameters}`
parameters_args <- c(list(model), params$parameters_args)
# add verbose, if not done yet
if (is.null(parameters_args$verbose)) parameters_args$verbose <- FALSE
table_parameters <- do.call(parameters::parameters, parameters_args)
plot(table_parameters)
```
```{r easydashboard-5, eval=!is_supported}
cat(unsupported_message)
```
Column {data-width=450}
-----------------------------------------------------------------------
### Tabular summary
```{r easydashboard-6, eval=is_supported}
print_md(table_parameters, caption = NULL)
```
```{r easydashboard-7, eval=!is_supported}
cat(unsupported_message)
```
To find out more about table summary options, please refer to <a href="https://easystats.github.io/parameters/reference/model_parameters.html" target="_blank">this documentation</a>.
Predicted Values
=====================================
Column {data-width=600}
-----------------------------------------------------------------------
### Plot
```{r expected-values, eval=is_supported, fig.height=10, fig.width=10}
# {modelbased}
int_terms <- find_interactions(model, component = "conditional", flatten = TRUE)
con_terms <- find_variables(model)$conditional
if (is.null(int_terms)) {
model_terms <- con_terms
} else {
model_terms <- clean_names(int_terms)
int_terms <- unique(unlist(strsplit(clean_names(int_terms), ":", fixed = TRUE)))
model_terms <- c(model_terms, setdiff(con_terms, int_terms))
}
# check some exceptions here: logistic regression models with factor response
# usually require the response to be included in the model, else `get_modelmatrix()`
# fails, which is required to compute SE/CI for `get_predicted()`
response <- find_response(model)
minfo <- model_info(model)
model_data <- get_data(model)
include_response <- minfo$is_binomial && minfo$is_logit && is.factor(model_data[[response]])
text_modelbased <- tryCatch(
{
lapply(unique(model_terms), function(i) {
dgrid <- get_datagrid(
model,
by = i,
range = "grid",
preserve_range = FALSE,
verbose = FALSE,
include_response = include_response
)
estimate_expectation(model, data = dgrid, verbose = FALSE)
})
},
error = function(e) {
cat(insight::format_message(
"\nSomething did not work as expected. Please file an issue at {.url https://github.com/easystats/easystats/issues/} and post the following output:",
paste0("\n`", e$message, "`")
))
NULL
}
)
if (!is.null(text_modelbased)) {
ggplot2::theme_set(theme_modern())
# all_plots <- lapply(text_modelbased, function(i) {
# out <- do.call(visualisation_recipe, c(list(i), modelbased_args))
# plot(out) + ggplot2::ggtitle("")
# })
all_plots <- lapply(text_modelbased, function(i) {
out <- visualisation_recipe(i, show_data = "none")
plot(out) + ggplot2::ggtitle("")
})
see::plots(all_plots, n_columns = round(sqrt(length(text_modelbased))))
}
```
```{r easydashboard-8, eval=!is_supported}
cat(unsupported_message)
```
Column {data-width=400}
-----------------------------------------------------------------------
### Tabular summary
```{r easydashboard-9, eval=is_supported, results="asis"}
if (!is.null(text_modelbased)) {
for (i in text_modelbased) {
tmp <- print_md(i)
tmp <- gsub("Variable predicted", "\nVariable predicted", tmp, fixed = TRUE)
tmp <- gsub("Predictors modulated", "\nPredictors modulated", tmp, fixed = TRUE)
tmp <- gsub("Predictors controlled", "\nPredictors controlled", tmp, fixed = TRUE)
print(tmp)
}
}
```
```{r easydashboard-10, eval=!is_supported}
cat(unsupported_message)
```
Text reports
=====================================
Column {data-width=500}
-----------------------------------------------------------------------
### Textual summary
```{r easydashboard-11, eval=is_supported, results='asis', collapse=TRUE}
# {report}
text_report <- tryCatch(
{
report(model, verbose = FALSE)
},
error = function(e) {
cat(insight::format_message(
"\nSomething did not work as expected. Please file an issue at {.url https://github.com/easystats/easystats/issues/} and post the following output:",
paste0("\n`", e$message, "`")
))
NULL
}
)
text_report_performance <- tryCatch(
{
report_performance(model, verbose = FALSE)
},
error = function(e) {
cat(insight::format_message(
"\nSomething did not work as expected. Please file an issue at {.url https://github.com/easystats/easystats/issues/} and post the following output:",
paste0("\n`", e$message, "`")
))
NULL
}
)
if (!is.null(text_report)) {
cat(bracket_to_parantheses(text_report))
cat("\n")
}
if (!is.null(text_report_performance)) {
cat(bracket_to_parantheses(text_report_performance))
}
```
```{r easydashboard-12, eval=!is_supported}
cat(unsupported_message)
```
Column {data-width=500}
-----------------------------------------------------------------------
### Model information
```{r easydashboard-13, eval=is_supported}
model_info_data <- insight::model_info(model, verbose = FALSE)
model_info_data <- datawizard::data_to_long(as.data.frame(insight::compact_list(model_info_data)))
DT::datatable(model_info_data)
```
```{r easydashboard-14, eval=!is_supported}
cat(unsupported_message)
```